From 2ee0007509d6038ff30e6572d4a26dc9443e301f Mon Sep 17 00:00:00 2001 From: Martin Weise <martin.weise@tuwien.ac.at> Date: Fri, 16 Dec 2022 14:30:22 +0100 Subject: [PATCH] Updated the docker images documentation --- dockerhub/fda-analyse-service.md | 26 ++++++++++++-- dockerhub/fda-authentication-service.md | 38 +++++++++++--------- dockerhub/fda-broker-service.md | 4 +-- dockerhub/fda-container-service.md | 22 +++++++++--- dockerhub/fda-database-service.md | 18 +++++++--- dockerhub/fda-discovery-service.md | 12 ++++--- dockerhub/fda-docs.md | 9 ----- dockerhub/fda-gateway-service.md | 14 +++++--- dockerhub/fda-identifier-service.md | 16 ++++++--- dockerhub/fda-query-service.md | 29 +++++++++++---- dockerhub/fda-search-service.md | 11 ------ dockerhub/fda-table-service.md | 18 ++++++---- dockerhub/fda-ui.md | 42 +++++++++------------- dockerhub/fda-units-service.md | 48 +++++++++++++++++++++++-- 14 files changed, 201 insertions(+), 106 deletions(-) delete mode 100644 dockerhub/fda-docs.md delete mode 100644 dockerhub/fda-search-service.md diff --git a/dockerhub/fda-analyse-service.md b/dockerhub/fda-analyse-service.md index 9f11cf6..d6e1551 100644 --- a/dockerhub/fda-analyse-service.md +++ b/dockerhub/fda-analyse-service.md @@ -8,8 +8,30 @@ $ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -p 5000:5 Change the default behavior by setting the following environment variables to different values: -* `EUREKA_SERVER` default: http://discovery-service:9090/eureka/, needs to point to - the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service). +* `FLASK_APP`, default: `app.py` + + The file that represents a flask app in the container. + +* `FLASK_RUN_HOST`, default: `0.0.0.0` + + The bind address for the flask server. + +* `PORT_APP`, default: `5000` + + The bind port for the flask server. + +* `FLASK_ENV`, default: `production` + + The flask environment mode. + +* `HOSTNAME`, default: `analyse-service` + + The name that is used at the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service) to register the + Analyse Service. + +* `EUREKA_SERVER`, default: `http://discovery-service:9090/eureka/` + + Needs to point to the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service). ## Swagger Endpoints diff --git a/dockerhub/fda-authentication-service.md b/dockerhub/fda-authentication-service.md index 8de21c5..2c7ccb4 100644 --- a/dockerhub/fda-authentication-service.md +++ b/dockerhub/fda-authentication-service.md @@ -8,79 +8,83 @@ $ docker run -p 9097:9097 -e SPRING_PROFILES_ACTIVE=docker Change the default behavior by setting the following environment variables to different values: -* `METADATA_DB`, default: fda +* `METADATA_DB`, default: `fda` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `dbrepo` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. -* `BROKER_USERNAME`, default: fda +* `BROKER_USERNAME`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags associated to the account. -* `BROKER_PASSWORD`, default: fda +* `BROKER_PASSWORD`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags associated to the account. -* `WEBSITE`, default: http://example.com +* `WEBSITE`, default: `http://example.com` The public endpoint of the [User Interface](https://hub.docker.com/r/dbrepo/ui). Internally, it is used to redirect when a user verifies the e-mail address. -* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095 +* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095` The gateway endpoint. -* `MAIL_FROM`, default: "Database Repository <noreply@example.com>" +* `MAIL_FROM`, default: `Database Repository <noreply@example.com>` When users verify their e-mail addresses, this is used to declare where the mail is coming from. -* `MAIL_REPLY_TO`, default: "Somebody <somebody@example.com>" +* `MAIL_REPLY_TO`, default: `Somebody <somebody@example.com>` When users verify their e-mail addresses, this is used to declare where to reply to. -* `MAIL_VERIFY`, default: false +* `MAIL_VERIFY`, default: `false` When set to `1`, the service requires all users to verify their e-mail before they can use the repository system, e.g. they cannot log in without clicking the link in the e-mail. -* `JWT_ISSUER`, default: dbrepo +* `JWT_ISSUER`, default: `dbrepo` The Java Web Token issuer name. -* `JWT_SECRET`, default: secret +* `JWT_SECRET`, default: `secret` The Java Web Token secret that is used to sign the token generated by the system. This should be treated like with the same caution as a private key. -* `JWT_EXPIRATION`, default: 86400000 +* `JWT_EXPIRATION`, default: `86400000` By default, the Java Web Token expire after 1 day. -* `SMTP_HOST`, optional. +* `SMTP_HOST`, optional The e-mail server that sends e-mails to the users. Specify the hostname. -* `SMTP_PORT`, optional. +* `SMTP_PORT`, optional The e-mail server that sends e-mails to the users. Specify the port. -* `SMTP_USERNAME`, optional. +* `SMTP_USERNAME`, optional The e-mail server that sends e-mails to the users. Specify the username. -* `SMTP_PASSWORD`, optional. +* `SMTP_PASSWORD`, optional The e-mail server that sends e-mails to the users. Specify the password. +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. + ## Swagger Endpoints * **OpenAPI**: diff --git a/dockerhub/fda-broker-service.md b/dockerhub/fda-broker-service.md index 1f28834..4a0a79e 100644 --- a/dockerhub/fda-broker-service.md +++ b/dockerhub/fda-broker-service.md @@ -8,11 +8,11 @@ $ docker run -v ./fda-broker-service-data:/var/lib/rabbitmq/ -p 9098:9098 -p 567 Change the default behavior by setting the following variables in `rabbitmq.conf` to different values: -* `default_user`, default: fda +* `default_user`, default: `fda` The Broker Service username. -* `default_pass`, default: fda +* `default_pass`, default: `fda` The Broker Service password. diff --git a/dockerhub/fda-container-service.md b/dockerhub/fda-container-service.md index 9057cba..1e1f3ed 100644 --- a/dockerhub/fda-container-service.md +++ b/dockerhub/fda-container-service.md @@ -8,28 +8,40 @@ $ docker run -p 9091:9091 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING Change the default behavior by setting the following environment variables to different values: -* `METADATA_DB`, default: fda +* `METADATA_DB`, default: `fda` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `mariadb` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. -* `BROKER_USERNAME`, default: fda +* `BROKER_USERNAME`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags associated to the account. -* `BROKER_PASSWORD`, default: fda +* `BROKER_PASSWORD`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags associated to the account. +* `SHARED_FILESYSTEM`, default: `/tmp` + + The folder that has a shared filesystem among services. + +* `USER_NETWORK`, default: `userdb` + + The Docker network that user-generated databases are connected to when created. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. + ## Swagger Endpoints * **OpenAPI**: diff --git a/dockerhub/fda-database-service.md b/dockerhub/fda-database-service.md index a2c6a91..bd7ed8d 100644 --- a/dockerhub/fda-database-service.md +++ b/dockerhub/fda-database-service.md @@ -8,32 +8,40 @@ $ docker run -p 9092:9092 -v /var/run/docker.sock:/var/run/docker.sock -e SPRING Change the default behavior by setting the following environment variables to different values: -* `METADATA_DB`, default: fda +* `METADATA_DB`, default: `fda` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `mariadb` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. -* `BROKER_USERNAME`, default: fda +* `BROKER_USERNAME`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags associated to the account. -* `BROKER_PASSWORD`, default: fda +* `BROKER_PASSWORD`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags associated to the account. +* `SEARCH_ENDPOINT`, default `search-service` + + Container hostname of the Search Service. + * `GATEWAY_ENDPOINT`, default: http://gateway-service:9095 The gateway endpoint. +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. + ## Swagger Endpoints * **OpenAPI**: diff --git a/dockerhub/fda-discovery-service.md b/dockerhub/fda-discovery-service.md index 627ef21..fdc99ce 100644 --- a/dockerhub/fda-discovery-service.md +++ b/dockerhub/fda-discovery-service.md @@ -8,14 +8,18 @@ $ docker run -p 9090:9090 -e SPRING_PROFILES_ACTIVE=docker Change the default behavior by setting the following environment variables to different values: -* `METADATA_DB`, default: fda +* `METADATA_DB`, default: `fda` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `dbrepo` - The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. \ No newline at end of file + The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. \ No newline at end of file diff --git a/dockerhub/fda-docs.md b/dockerhub/fda-docs.md deleted file mode 100644 index 262f431..0000000 --- a/dockerhub/fda-docs.md +++ /dev/null @@ -1,9 +0,0 @@ -# How to use this image - -```console -$ docker run -p 80:80 -``` - -## Customization - -No customization. \ No newline at end of file diff --git a/dockerhub/fda-gateway-service.md b/dockerhub/fda-gateway-service.md index 09911f6..df9bf11 100644 --- a/dockerhub/fda-gateway-service.md +++ b/dockerhub/fda-gateway-service.md @@ -8,18 +8,22 @@ $ docker run -p 9095:9095 -e SPRING_PROFILES_ACTIVE=docker Change the default behavior by setting the following environment variables to different values: -* `METADATA_DB`, default: fda +* `METADATA_DB`, default: `fda` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `mariadb` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. -* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095 +* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095` - The gateway endpoint. \ No newline at end of file + The gateway endpoint. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. \ No newline at end of file diff --git a/dockerhub/fda-identifier-service.md b/dockerhub/fda-identifier-service.md index 70d65f8..96d413c 100644 --- a/dockerhub/fda-identifier-service.md +++ b/dockerhub/fda-identifier-service.md @@ -8,22 +8,30 @@ $ docker run -p 9096:9096 -e SPRING_PROFILES_ACTIVE=docker Change the default behavior by setting the following environment variables to different values: -* `METADATA_DB`, default: fda +* `METADATA_DB`, default: `fda` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `dbrepo` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. -* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095 +* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095` The gateway endpoint. +* `WEBSITE`, default: `http://localhost:3000` + + The absolute url to the front end for redirecting PID lookups. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. + ## Swagger Endpoints * **OpenAPI**: diff --git a/dockerhub/fda-query-service.md b/dockerhub/fda-query-service.md index 6b12bc5..7fcb9c6 100644 --- a/dockerhub/fda-query-service.md +++ b/dockerhub/fda-query-service.md @@ -8,32 +8,49 @@ $ docker run -p 9093:9093 -e SPRING_PROFILES_ACTIVE=docker Change the default behavior by setting the following environment variables to different values: -* `METADATA_DB`, default: fda +* `METADATA_DB`, default: `fda` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `dbrepo` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. -* `BROKER_USERNAME`, default: fda +* `BROKER_USERNAME`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags associated to the account. -* `BROKER_PASSWORD`, default: fda +* `BROKER_PASSWORD`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags associated to the account. -* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095 +* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095` The gateway endpoint. +* `SHARED_FILESYSTEM`, default: `/tmp` + + The folder that has a shared filesystem among services. + +* `BROKER_CONSUMERS`, default: `2` + + Number of consumers each queue in the [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) should + maintain in the Query Service. Minimum 1. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. + +* `NOT_SUPPORTED_KEYWORDS`, default: `*,AVG,BIT_AND,BIT_OR,BIT_XOR,COUNT,COUNTDISTINCT,GROUP_CONCAT,JSON_ARRAYAGG,JSON_OBJECTAGG,MAX,MIN,STD,STDDEV,STDDEV_POP,STDDEV_SAMP,SUM,VARIANCE,VAR_POP,VAR_SAMP,--` + + Comma-separated list of (key-)words that are not allowed in any query or view. The case does not matter. + ## Swagger Endpoints * **OpenAPI**: diff --git a/dockerhub/fda-search-service.md b/dockerhub/fda-search-service.md deleted file mode 100644 index 7b6a38a..0000000 --- a/dockerhub/fda-search-service.md +++ /dev/null @@ -1,11 +0,0 @@ -# How to use this image - -```console -$ docker run -p 9200:9200 -p 9600:9600 -e discovery.type=single-node -e "ES_JAVA_OPTS=-Xms512m -Xmx512m" -e logger.level=WARN -``` - -## ElasticSearch Endpoints - -* **Database Index**: - - http://localhost:9000/databaseindex diff --git a/dockerhub/fda-table-service.md b/dockerhub/fda-table-service.md index a6e8653..429bddb 100644 --- a/dockerhub/fda-table-service.md +++ b/dockerhub/fda-table-service.md @@ -12,31 +12,35 @@ Change the default behavior by setting the following environment variables to di The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. -* `METADATA_USERNAME`, default: postgres +* `METADATA_USERNAME`, default: `root` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. -* `METADATA_PASSWORD`, default: postgres +* `METADATA_PASSWORD`, default: `dbrepo` The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. -* `BROKER_USERNAME`, default: fda +* `BROKER_USERNAME`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags associated to the account. -* `BROKER_PASSWORD`, default: fda +* `BROKER_PASSWORD`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags associated to the account. -* `GATEWAY_ENDPOINT`, default: http://gateway-service:9095 +* `GATEWAY_ENDPOINT`, default: `http://gateway-service:9095` The gateway endpoint. -* `multipart.location`, default: /tmp +* `multipart.location`, default: `/tmp` - The shared file-system directory where the temporary files are stored to for the front-end and the .csv import. + The folder that has a shared filesystem among services. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. ## Swagger Endpoints diff --git a/dockerhub/fda-ui.md b/dockerhub/fda-ui.md index b40cc26..b0b01f7 100644 --- a/dockerhub/fda-ui.md +++ b/dockerhub/fda-ui.md @@ -8,55 +8,45 @@ $ docker run -v /tmp:/tmp -p 3000:3000 -e HOST=0.0.0.0 -e API=http://fda-gateway Change the default behavior by setting the following environment variables to different values: -* `API`, default: http://gateway-service:9095 +* `API`, default: `http://gateway-service:9095` The [Gateway Service](https://hub.docker.com/r/dbrepo/gateway-service) endpoint. -* `BROKER_USERNAME`, default: fda +* `BROKER_USERNAME`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) username of a user that has `administrator` tags associated to the account. -* `BROKER_PASSWORD`, default: fda +* `BROKER_PASSWORD`, default: `fda` The [Broker Service](https://hub.docker.com/r/dbrepo/broker-service) password of a user that has `administrator` tags associated to the account. -* `SANDBOX`, default: false +* `SANDBOX`, default: `false` When set to `1`, the interface displays a warning not to include production data. -* `KEY`, optional. +* `SEARCH`, default: `http://search-service:9200` - The private key of an SSL/TLS certificate to be used by the webserver. The key needs to be a single-line string and + The endpoint of the Search Service. - ```console - $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/privkey.pem - ``` +* `SHARED_FILESYSTEM`, default: `/tmp` -* `CERT`, optional. + The folder that has a shared filesystem among services. - The SSL/TLS certificate to be used by the webserver. The certificate needs to be a single-line string and can be - easily prepared by the command line: +* `VERSION`, default: `1.1` - ```console - $ sed -E ':a;N;$!ba;s/\r{0,1}\n/\\n/g' /path/to/cert.pem - ``` + The version number to display on the left navigation drawer. -* `LOGO`, optional. +* `LOGO`, default: `/logo.png` - Relative path to the graphics that should be displayed as a logo in the left pane. The path is relative to the mount - point in the `docker-compose.yml` file. For example add in the `docker-compose.yml`: + The file that is used to display the logo on the left navigation drawer. Tip: place the file in `/app`. - ```yaml - fda-ui: - ... - volumes: - - /tmp:/tmp - - /path/to/logo.png:/app/static/logo.png:ro # <<< add this line pointing to your local logo.png file - ``` +* `MAIL_VERIFY`, default: `false` - And place the logo on the host at `/logos/logo.png`, then set the value of `LOGO` to `/logos/logo.png` + If set to `true`, a mail will be sent via + the [Authentication Service](https://hub.docker.com/r/dbrepo/authentication-service) endpoint and it will be mandatory + to click a link in the e-mail before proceeding to login. ## Graphical Endpoints diff --git a/dockerhub/fda-units-service.md b/dockerhub/fda-units-service.md index f36edd7..150b158 100644 --- a/dockerhub/fda-units-service.md +++ b/dockerhub/fda-units-service.md @@ -8,8 +8,50 @@ $ docker run -p 5010:5010 -e SPRING_PROFILES_ACTIVE=docker Change the default behavior by setting the following environment variables to different values: -* `EUREKA_SERVER` default: http://discovery-service:9090/eureka/, needs to point to - the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service). +* `FLASK_APP`, default: `app.py` + + The file that represents a flask app in the container. + +* `FLASK_RUN_HOST`, default: `0.0.0.0` + + The bind address for the flask server. + +* `PORT_APP`, default: `5010` + + The bind port for the flask server. + +* `FLASK_ENV`, default: `production` + + The flask environment mode. + +* `HOSTNAME`, default: `units-service` + + The name that is used at the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service) to register the + Units Service. + +* `EUREKA_SERVER`, default: `http://discovery-service:9090/eureka/` + + Needs to point to the [Discovery Service](https://hub.docker.com/r/dbrepo/discovery-service). + +* `READY_FILE`, default: `/ready` + + The full path to the file with filename where to place a file when the service is ready. + +* `LOG_LEVEL`, default: `debug` + + The minimum logging level for the service. + +* `METADATA_DB`, default: `fda` + + The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database name. + +* `METADATA_USERNAME`, default: `root` + + The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database username. + +* `METADATA_PASSWORD`, default: `mariadb` + + The [Metadata Database](https://hub.docker.com/r/dbrepo/metadata-db) database password. ## Swagger Endpoints @@ -18,5 +60,5 @@ Change the default behavior by setting the following environment variables to di http://localhost:5010/swagger-ui/ * **OpenAPI `.json`**: - + http://localhost:5010/api-analyze.json -- GitLab